When the Civil War erupted in 1861, Garrard, by then a captain, was on duty in an outpost in Texas. As a loyal Unionist, he was imprisoned by Confederate authorities following the surrender of U.S. troops by Maj. Gen. David E. Twiggs. He was allowed to travel back to the North. He made his way to Washington, D.C., bringing with him $20,000 of Federal funds he had secreted from Texas, returning the money to the U.S. Treasury. In December 1861, he was appointed as Commandant of the U.S. Military Academy in West Point, New York.

He was appointed as the major of the 3rd U.S. Cavalry in the regular army in November 1863, while continuing to hold the rank of brigadier general in the volunteer army. In December 1863, he was made Chief of the Cavalry Bureau in Washington, but was the next month, at his own request, relieved from that duty to take command of the 2nd Division of Cavalry in the Army of the Cumberland, and transferred to the Western Theater.

Garrard took part in Sherman's Atlanta Campaign as a cavalry division commander, but failed to impress his superiors. Returning to the infantry, he participated in the Battle of Nashville, where he and his division performed well. Army commander Maj. Gen. George H. Thomas cited Garrard for gallant conduct at Nashville. As a result, he was appointed a brevet major general of volunteers and brevet brigadier general in the regular army for his battlefield performance. He also received the brevet rank of major general in the regular army as of March 13, 1865, as part of the mass brevet appointments at the end of the war.[2] He ended the war in Alabama and was instrumental in the capture of Montgomery.

Garrard remained in the regular army after the war ended as commander of the District of Mobile, but resigned on November 9, 1866. He returned to Cincinnati where he worked as a real estate broker.[2] He devoted the rest of his life to civic affairs and historical studies. He served as Director of the Cincinnati Music Festival for several years. He never married.